Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004850.1 Hibiscus syriacus cultivar Beakdansim tig00010931_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 73506
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.32
Found at i:611 original size:106 final size:104
Alignment explanation
Indices: 431--633 Score: 338
Period size: 106 Copynumber: 1.9 Consensus size: 104
421 GATTGTTTAC
431 ATTTGTGTCAATTTTAGGCTAACTTATAAGTGTTTCCATATTCTTGTATAGTTGACTTTCCTATT
1 ATTTGTGTCAATTTTAGGCTAACTTATAAGTGTTTCCATATTCTTGTATA--TGACTTTCCTATT
496 AAGACTCTTGAATATATATAATATAGGTCCCTAAGTTTTACAA
64 AAGACTCTTGAATATATAT-ATATA-GTCCCTAAGTTTTACAA
539 ATTTGTGTCAATTTATAGGCTAACTTATAAGT-TTTCCATATTTCTTGTATA-GACTTTCCTATT
1 ATTTGTGTCAATTT-TAGGCTAACTTATAAGTGTTTCCATA-TTCTTGTATATGACTTTCCTATT
602 AAGACTCTTGAATATATATATATAGTCCCTAA
64 AAGACTCTTGAATATATATATATAGTCCCTAA
634 AGTTGTAATC
Statistics
Matches: 93, Mismatches: 0, Indels: 8
0.92 0.00 0.08
Matches are distributed among these distances:
104 8 0.09
105 5 0.05
106 31 0.33
108 22 0.24
109 27 0.29
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.44
Consensus pattern (104 bp):
ATTTGTGTCAATTTTAGGCTAACTTATAAGTGTTTCCATATTCTTGTATATGACTTTCCTATTAA
GACTCTTGAATATATATATATAGTCCCTAAGTTTTACAA
Found at i:2106 original size:12 final size:12
Alignment explanation
Indices: 2040--2106 Score: 52
Period size: 12 Copynumber: 5.8 Consensus size: 12
2030 TATTCACGAA
*
2040 CAACTCATTTAT
1 CAACTCGTTTAT
*
2052 GAACTCGTTTAT
1 CAACTCGTTTAT
*
2064 C-ACTTGTTTAT
1 CAACTCGTTTAT
*
2075 -AAGCTTG-TTA-
1 CAA-CTCGTTTAT
2085 CAAGCTCGTTTAT
1 CAA-CTCGTTTAT
2098 CAACTCGTT
1 CAACTCGTT
2107 CATCTATGTT
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
11 19 0.42
12 23 0.51
13 3 0.07
ACGTcount: A:0.25, C:0.21, G:0.12, T:0.42
Consensus pattern (12 bp):
CAACTCGTTTAT
Found at i:15341 original size:16 final size:16
Alignment explanation
Indices: 15316--15376 Score: 86
Period size: 16 Copynumber: 3.8 Consensus size: 16
15306 TAATAAATAA
*
15316 ACGAATATAAACGAAC
1 ACGAACATAAACGAAC
*
15332 ACGAACATAAAAGAAC
1 ACGAACATAAACGAAC
* *
15348 ACAAACATAAATGAAC
1 ACGAACATAAACGAAC
15364 ACGAACATAAACG
1 ACGAACATAAACG
15377 TTGGAGACCC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.59, C:0.20, G:0.11, T:0.10
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:19534 original size:24 final size:24
Alignment explanation
Indices: 19473--19527 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
19463 TATTATGTTA
19473 AACATAAACGAACGCACATAAACG
1 AACATAAACGAACGCACATAAACG
** *
19497 AACATAATTGAACGCATATAAACG
1 AACATAAACGAACGCACATAAACG
19521 AACATAA
1 AACATAA
19528 CCAAACGTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.55, C:0.20, G:0.11, T:0.15
Consensus pattern (24 bp):
AACATAAACGAACGCACATAAACG
Found at i:21637 original size:149 final size:149
Alignment explanation
Indices: 21367--21819 Score: 888
Period size: 149 Copynumber: 3.0 Consensus size: 149
21357 CAAAGTGCCC
* *
21367 CGTAGAATTGCATCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
21432 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
21497 CATATGTCCCGAAGAACCG
131 CATATGTCCCGAAGAACCG
21516 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
21581 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
21646 CATATGTCCCGAAGAACCG
131 CATATGTCCCGAAGAACCG
21665 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
21730 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
21795 CATATGTCCCGAAGAACCG
131 CATATGTCCCGAAGAACCG
21814 CGTAGA
1 CGTAGA
21820 CCCTCGACTC
Statistics
Matches: 302, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 302 1.00
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.28
Consensus pattern (149 bp):
CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
CATATGTCCCGAAGAACCG
Found at i:22723 original size:18 final size:18
Alignment explanation
Indices: 22702--22736 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
22692 TCCCATCTAG
22702 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
22720 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
22737 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:23344 original size:21 final size:21
Alignment explanation
Indices: 23320--23364 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
23310 TCTTGTTCGT
* *
23320 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
23341 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
23362 TTG
1 TTG
23365 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:26665 original size:149 final size:149
Alignment explanation
Indices: 26395--26847 Score: 888
Period size: 149 Copynumber: 3.0 Consensus size: 149
26385 CAAAGTGCCC
* *
26395 CGTAGAATTGCATCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
26460 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
26525 CATATGTCCCGAAGAACCG
131 CATATGTCCCGAAGAACCG
26544 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
26609 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
26674 CATATGTCCCGAAGAACCG
131 CATATGTCCCGAAGAACCG
26693 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
26758 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
26823 CATATGTCCCGAAGAACCG
131 CATATGTCCCGAAGAACCG
26842 CGTAGA
1 CGTAGA
26848 CCCTCGACTC
Statistics
Matches: 302, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 302 1.00
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.28
Consensus pattern (149 bp):
CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
CATATGTCCCGAAGAACCG
Found at i:27752 original size:18 final size:18
Alignment explanation
Indices: 27731--27765 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
27721 TCCCATCTAG
27731 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
27749 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
27766 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:28378 original size:21 final size:21
Alignment explanation
Indices: 28348--28392 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
28338 TCTTGTTCGT
* *
28348 TTGAAGGGGTATCGTTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
28369 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
28390 TTG
1 TTG
28393 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.27, T:0.33
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:31634 original size:3 final size:3
Alignment explanation
Indices: 31626--31702 Score: 79
Period size: 3 Copynumber: 26.0 Consensus size: 3
31616 ATTATTCTTT
* *
31626 TAA TAA TAA TAA TAA T-A TATA TAT TAA -AA T-A TATA TAA TAA TTA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TA-A TAA TAA TAA
* *
31670 TAA TAA TAA TTA TTA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
31703 ATAAATAAAT
Statistics
Matches: 63, Mismatches: 6, Indels: 10
0.80 0.08 0.13
Matches are distributed among these distances:
2 6 0.10
3 51 0.81
4 6 0.10
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:31997 original size:39 final size:40
Alignment explanation
Indices: 31954--32049 Score: 131
Period size: 40 Copynumber: 2.4 Consensus size: 40
31944 TTGAACAAGC
*
31954 TCTTCTCATTGTGAACTTCTTCTTC-CTCTCCAGATAAGT
1 TCTTCTCATTATGAACTTCTTCTTCTCTCTCCAGATAAGT
* * * * *
31993 TCTTCTCATTATAAACTTCTTCTTCTTTCTTCAGGTGAGT
1 TCTTCTCATTATGAACTTCTTCTTCTCTCTCCAGATAAGT
32033 TCTTCTCATTATGAACT
1 TCTTCTCATTATGAACT
32050 CTACCTGGCA
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
39 23 0.47
40 26 0.53
ACGTcount: A:0.19, C:0.25, G:0.09, T:0.47
Consensus pattern (40 bp):
TCTTCTCATTATGAACTTCTTCTTCTCTCTCCAGATAAGT
Found at i:32196 original size:116 final size:113
Alignment explanation
Indices: 31989--32646 Score: 968
Period size: 113 Copynumber: 5.8 Consensus size: 113
31979 CTCTCCAGAT
* * *
31989 AAGTTCTTCTCATTATAAACTTCTTCTTCTTTCTTCAGGTGAGTTCTTCTCATTATGAACTCTAC
1 AAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAC
* * * *
32054 CTGGCAATGCTGATCCATCAAATGATGAATTCAAAC-AAAAGGTTGAAC
66 CTGGAAATGTTGATCCATCGAATGATGAATTCAAGCGAAAA-GTTGAAC
* *
32102 AAATTATTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTC
1 AAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAACTC
*
32167 TACCTGGTAATGTTGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAAC
63 TACCTGGAAATGTTGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAAC
*
32218 AAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC-CT-G
1 AAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAC
* * * *
32281 CTGGTAACGCTGATCCATCGAATGATGAATTCGAGC-AAAAGGTTGAAC
66 CTGGAAATGTTGATCCATCGAATGATGAATTCAAGCGAAAA-GTTGAAC
* *
32329 AAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT-TTC
1 AAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAC
*
32393 TCTGGAAAAGTTGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAAC
66 -CTGGAAATGTTGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAAC
* * *
32442 AAGTTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTGATTATGAAC-CTGC
1 AAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAC
*
32506 TCTGGAAAAGTTGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAAC
66 -CTGGAAATGTTGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAAC
* *
32555 AAGTTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAC
1 AAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAC
* * *
32620 CTGGCAATGTTGATCCACCGAGTGATG
66 CTGGAAATGTTGATCCATCGAATGATG
32647 GATTTTAATC
Statistics
Matches: 502, Mismatches: 32, Indels: 22
0.90 0.06 0.04
Matches are distributed among these distances:
110 4 0.01
111 100 0.20
112 2 0.00
113 284 0.57
114 6 0.01
116 102 0.20
117 4 0.01
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.37
Consensus pattern (113 bp):
AAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAC
CTGGAAATGTTGATCCATCGAATGATGAATTCAAGCGAAAAGTTGAAC
Found at i:32610 original size:337 final size:338
Alignment explanation
Indices: 31992--32614 Score: 1020
Period size: 340 Copynumber: 1.8 Consensus size: 338
31982 TCCAGATAAG
* *
31992 TTCTTCTCATTATAAACTTCTTCTTCTTTCTTCAGGTGAGTTCTTCTCATTATGAACTCTACCTG
1 TTCTTCTCATTATAAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTG
* *
32057 GCAATGCTGATCCATCAAATGATGAATTCAAACAAAAGGTTGAACAAATTATTCTCATTATGAAC
66 GAAAAGCTGATCCATCAAATGATGAATTCAAACAAAAGGTTGAACAAATTATTCTCATTATGAAC
* *
32122 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGTAATGTTGATCCA
131 TTCTTCTTCCTTCTTCAGAT-A-GAGTTCTTCTCATTATGAACTCTACCTGGAAAAGTTGATCCA
32187 TCGAATGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCT
194 TCGAATGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCT
32252 TCAGATGAGTTCTTCTCATTATGAACCTGCTGGTAACGCTGATCCATCGAATGATGAATTCGAGC
259 TCAGATGAGTTCTTCTCATTATGAACCTGCTGGTAACGCTGATCCATCGAATGATGAATTCGAGC
32317 AAAAGGTTGAACAAA
324 AAAAGGTTGAACAAA
* *
32332 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT-TTCTCT
1 TTCTTCTCATTATAAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAC-CT
* * * * *
32396 GGAAAAGTTGATCCATCGAATGATGAATTCAAGCGAAAA-GTTGAACAAGTTCTTCTCATTATGA
65 GGAAAAGCTGATCCATCAAATGATGAATTCAAAC-AAAAGGTTGAACAAATTATTCTCATTATGA
* * *
32460 ACTTCTTCTTTCTTCTTCAGAT-GAGTTCTTCTGATTATGAAC-CTGCTCTGGAAAAGTTGATCC
129 ACTTCTTCTTCCTTCTTCAGATAGAGTTCTTCTCATTATGAACTCTAC-CTGGAAAAGTTGATCC
*
32523 ATCGAATGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTTCTTC
193 ATCGAATGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTC
32588 TTCAGATGAGTTCTTCTCATTATGAAC
258 TTCAGATGAGTTCTTCTCATTATGAAC
32615 TCGACCTGGC
Statistics
Matches: 263, Mismatches: 17, Indels: 9
0.91 0.06 0.03
Matches are distributed among these distances:
336 3 0.01
337 124 0.47
339 2 0.01
340 130 0.49
341 4 0.02
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.37
Consensus pattern (338 bp):
TTCTTCTCATTATAAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTG
GAAAAGCTGATCCATCAAATGATGAATTCAAACAAAAGGTTGAACAAATTATTCTCATTATGAAC
TTCTTCTTCCTTCTTCAGATAGAGTTCTTCTCATTATGAACTCTACCTGGAAAAGTTGATCCATC
GAATGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTC
AGATGAGTTCTTCTCATTATGAACCTGCTGGTAACGCTGATCCATCGAATGATGAATTCGAGCAA
AAGGTTGAACAAA
Found at i:33483 original size:114 final size:114
Alignment explanation
Indices: 33320--33540 Score: 352
Period size: 114 Copynumber: 1.9 Consensus size: 114
33310 GATCATGCAG
* * * * * * *
33320 TTCATCTTTTAATTCCAATGATTGGTTCTGTGGTTCCTACCGAACCAGATCAGATGACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGATTCTGAGGTTCATACCAAACCAGATCAGATAACTCAAAGA
33385 AAACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
66 AAACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
* *
33434 TTCATCTTTCAAATCCAATGATTGATTTTGAGGTTCATACCAAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGATTCTGAGGTTCATACCAAACCAGATCAGATAACTCAAAGA
*
33499 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTAT
66 AAACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTAT
33541 AAGAACGTAG
Statistics
Matches: 97, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
114 97 1.00
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATTGATTCTGAGGTTCATACCAAACCAGATCAGATAACTCAAAGA
AAACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
Found at i:33866 original size:19 final size:17
Alignment explanation
Indices: 33838--33886 Score: 55
Period size: 16 Copynumber: 2.8 Consensus size: 17
33828 AAAATAAAAG
*
33838 AATAAGTTGAATTTTCGAA
1 AATAAATTGAATTTTC--A
*
33857 AATAAATTGAA-TCTCA
1 AATAAATTGAATTTTCA
33873 AATAAATTGAATTT
1 AATAAATTGAATTT
33887 AGAGAAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 12 0.46
17 1 0.04
18 3 0.12
19 10 0.38
ACGTcount: A:0.47, C:0.06, G:0.10, T:0.37
Consensus pattern (17 bp):
AATAAATTGAATTTTCA
Found at i:34242 original size:6 final size:6
Alignment explanation
Indices: 34220--34262 Score: 54
Period size: 6 Copynumber: 7.3 Consensus size: 6
34210 TTGACCCCTT
*
34220 TTTTTC TTTTT- TTTTTC TTTTTC TTCTTC TTTCTT- TTTTTC TT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTT-TTC TTTTTC TT
34263 CAAGCATAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
5 7 0.22
6 23 0.72
7 2 0.06
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTC
Found at i:34261 original size:15 final size:16
Alignment explanation
Indices: 34233--34263 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
34223 TTCTTTTTTT
34233 TTTCTTTTTCTTCTTC
1 TTTCTTTTTCTTCTTC
34249 TTTCTTTTT-TTCTTC
1 TTTCTTTTTCTTCTTC
34264 AAGCATAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTCTTTTTCTTCTTC
Found at i:46732 original size:3 final size:3
Alignment explanation
Indices: 46724--46798 Score: 91
Period size: 3 Copynumber: 25.0 Consensus size: 3
46714 ATTATTCTTT
46724 TAA TAA TAA TAA TAA T-A TATA TAA TAA T-A TATA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TA-A TAA TAA TAA TAA
* * *
46769 TTA TTA TAA TAA TTA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
46799 ATAAATAAAT
Statistics
Matches: 64, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
2 4 0.06
3 54 0.84
4 6 0.09
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:46762 original size:30 final size:30
Alignment explanation
Indices: 46724--46806 Score: 118
Period size: 30 Copynumber: 2.8 Consensus size: 30
46714 ATTATTCTTT
46724 TAATAATAATAATAATATATATAATAA-TA
1 TAATAATAATAATAATATATATAATAATTA
46753 TATATAATAATAATAAT-TATTATAATAATTA
1 TA-ATAATAATAATAATATA-TATAATAATTA
*
46784 TAATAATAATAATAA-ATAAATAA
1 TAATAATAATAATAATATATATAA
46807 ATAAAATGGG
Statistics
Matches: 49, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
29 8 0.16
30 37 0.76
31 4 0.08
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (30 bp):
TAATAATAATAATAATATATATAATAATTA
Found at i:47000 original size:2 final size:2
Alignment explanation
Indices: 46993--47052 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
46983 TTAATTTATG
46993 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
47035 TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
47053 AAAGATAGTA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:64865 original size:21 final size:21
Alignment explanation
Indices: 64839--64887 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
64829 TCTTGCGCTC
64839 TACCAACTGTAAGATATCCAT
1 TACCAACTGTAAGATATCCAT
64860 TACCAACTGTAAGATATCCAT
1 TACCAACTGTAAGATATCCAT
64881 TACCAAC
1 TACCAAC
64888 ATAGCAACCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.39, C:0.27, G:0.08, T:0.27
Consensus pattern (21 bp):
TACCAACTGTAAGATATCCAT
Found at i:68566 original size:24 final size:24
Alignment explanation
Indices: 68515--68568 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
68505 CGAACCTTTT
* * *
68515 AAGCTAACTTGTCAAAAATAAACC
1 AAGCTGACTTGTCAAAAAAAAACA
* *
68539 AAGCTGACTTTTCAAAAAAAAATA
1 AAGCTGACTTGTCAAAAAAAAACA
68563 AAGCTG
1 AAGCTG
68569 TCAGAAAATT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.50, C:0.17, G:0.11, T:0.22
Consensus pattern (24 bp):
AAGCTGACTTGTCAAAAAAAAACA
Found at i:70448 original size:15 final size:16
Alignment explanation
Indices: 70417--70449 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
70407 AAATTAAAAG
*
70417 AAAATAAAACATCATA
1 AAAATAAAACATAATA
70433 AAAATAAAACA-AATA
1 AAAATAAAACATAATA
70448 AA
1 AA
70450 TAAAGATGAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.76, C:0.09, G:0.00, T:0.15
Consensus pattern (16 bp):
AAAATAAAACATAATA
Found at i:70507 original size:45 final size:46
Alignment explanation
Indices: 70432--70529 Score: 105
Period size: 45 Copynumber: 2.2 Consensus size: 46
70422 AAAACATCAT
*
70432 AAAAATAAAACAAATAAATAAAGATGACAAAGA-ATAAT-AAATAAA
1 AAAAATAAAACAAATAAATAAAGATGACAAA-ATAAAATGAAATAAA
* * *
70477 TAAAATAAAACAAGT-AA-AATGCATGAACAAAATAAAATGAAATAAA
1 AAAAATAAAACAAATAAATAAAG-ATG-ACAAAATAAAATGAAATAAA
70523 AAAAATA
1 AAAAATA
70530 GAATTGTCAA
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
43 3 0.07
44 6 0.14
45 22 0.50
46 13 0.30
ACGTcount: A:0.71, C:0.05, G:0.07, T:0.16
Consensus pattern (46 bp):
AAAAATAAAACAAATAAATAAAGATGACAAAATAAAATGAAATAAA
Found at i:70594 original size:2 final size:2
Alignment explanation
Indices: 70587--70645 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
70577 AAAACAAGAA
70587 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
70629 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
70646 ATAATAAAAA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:72678 original size:121 final size:120
Alignment explanation
Indices: 72425--72722 Score: 355
Period size: 121 Copynumber: 2.4 Consensus size: 120
72415 GCTCCTTCGC
* * * *
72425 TGTGAAGTTGAGCTTTGAATTGAATATCCTCCGTCGTGAAGTTGAAATCTAATCTTAAGTTGTAT
1 TGTGAAGTTGAGC-TTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAA---TAAGTTGCAT
* * * * ** *
72490 GTTTCTTGTGGGCACGATATCCTTCATCGTGAAGTTGAAATCATGGATGGCTTCTTCGT
62 GCTGCTTGTAGGCACGATATCCTTCATCATGAAGTTGAAATCATGGATGGCCCCTTCAT
**
72549 TGTGAAGTTGAGCTTAGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAA-GGGTTGCATTGC
1 TGTGAAGTTGAGCTT-GAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATAAGTTGCA-TGC
* * * *
72613 TGCTTGTAGGTATGATATCCTTCGTCATGAAGTTGAAATCGTGGATGGCCCCTTCAT
64 TGCTTGTAGGCACGATATCCTTCATCATGAAGTTGAAATCATGGATGGCCCCTTCAT
**
72670 TGTGAAGTTGAGCCTTGAATTGGATATCCTTCACCGTGAAGTTGAAATCCAAT
1 TGTGAAGTTGAG-CTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAAT
72723 TTTGCTTCAC
Statistics
Matches: 151, Mismatches: 19, Indels: 10
0.84 0.11 0.06
Matches are distributed among these distances:
120 5 0.03
121 95 0.63
122 3 0.02
123 2 0.01
124 46 0.30
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.35
Consensus pattern (120 bp):
TGTGAAGTTGAGCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATAAGTTGCATGCTG
CTTGTAGGCACGATATCCTTCATCATGAAGTTGAAATCATGGATGGCCCCTTCAT
Found at i:72751 original size:121 final size:121
Alignment explanation
Indices: 72505--72771 Score: 330
Period size: 121 Copynumber: 2.2 Consensus size: 121
72495 TTGTGGGCAC
* ** *
72505 GATATCCTTCATCGTGAAGTTGAAATCATGGATGGCTTCTTCGTTGTGAAGTTGAGCTTAGAATT
1 GATATCCTTCGTCGTGAAGTTGAAATCATGGATGGCCCCTTCATTGTGAAGTTGAGCTTAGAATT
** **
72570 GGATATCCTTCGTCGTGAAGTTGAAATCCAAGGGTTGCATTGCTGCTTGTAGGTAT
66 GGATATCCTTCACCGTGAAGTTGAAATCCAAGGGTTGCATTGCACCTTGTAGGTAT
* *
72626 GATATCCTTCGTCATGAAGTTGAAATCGTGGATGGCCCCTTCATTGTGAAGTTGAGCCTT-GAAT
1 GATATCCTTCGTCGTGAAGTTGAAATCATGGATGGCCCCTTCATTGTGAAGTTGAG-CTTAGAAT
**
72690 TGGATATCCTTCACCGTGAAGTTGAAATCCAA-TTTTGC-TT-CACCAAATTGGT-GGT-T
65 TGGATATCCTTCACCGTGAAGTTGAAATCCAAGGGTTGCATTGCACC---TT-GTAGGTAT
72746 GGATATCCTTCGTCGTGAAGTTGAAA
1 -GATATCCTTCGTCGTGAAGTTGAAA
72772 CCCAATCTTT
Statistics
Matches: 127, Mismatches: 13, Indels: 12
0.84 0.09 0.08
Matches are distributed among these distances:
118 2 0.02
119 2 0.02
120 5 0.04
121 113 0.89
122 5 0.04
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (121 bp):
GATATCCTTCGTCGTGAAGTTGAAATCATGGATGGCCCCTTCATTGTGAAGTTGAGCTTAGAATT
GGATATCCTTCACCGTGAAGTTGAAATCCAAGGGTTGCATTGCACCTTGTAGGTAT
Found at i:72777 original size:55 final size:58
Alignment explanation
Indices: 72684--72839 Score: 192
Period size: 60 Copynumber: 2.7 Consensus size: 58
72674 AAGTTGAGCC
* **
72684 TTGAATTGGATATCCTTCACCGTGAAGTTGAAATCCAAT-TTTGCTTCACCAAATTGG
1 TTGAGTTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTTTGCTTCACCAAATTGG
* *
72741 -TG-GTTGGATATCCTTCGTCGTGAAGTTGAAACCCAATCTTTGTTTCACCAAATTGG
1 TTGAGTTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTTTGCTTCACCAAATTGG
* * * *
72797 CTTTGAGTTGGATATCATTTGTTGTGAAGTTAAAATCCAATCT
1 --TTGAGTTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCT
72840 CGAGTAAGTC
Statistics
Matches: 84, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
55 31 0.37
56 19 0.23
59 2 0.02
60 32 0.38
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.37
Consensus pattern (58 bp):
TTGAGTTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTTTGCTTCACCAAATTGG
Done.